[Nexus 6 Q&A, Help & Troubleshooting] scryan:
That is not even close to being true for basically any phone with TWRP/custom recovery.

The recovery loads well before the system, and is on a different partition. TWRP has supported sideloading for quite a few versions now, and any phone with an unlocked bootloader can likely use fastboot or an equivalent to rewrite the system from bootloader mode.

It's perfectly fine to not understand or not be informed... By why does every person who has little idea what they are doing have to over emphasise that they have been flashing for years? Its fine to have a gap in understanding or a lack of knowledge. Particularly with Android which is not as well documented as other systems... Even better to ask... But man everytime I read "I am not new at this, I have been flashing for years..." its followed by a fairly basic question.

So that I am not just *****ing, let me ramble about booting ... Read as much or as little as you like :P Anyone who wants to correct me please do, this will mostly be rough and loosely worded :)

Its important to understand that when turning on your phone, it doesn't just send electricity to Android, and spring to life.

If you think about it... If everything was fully shut down and lifeless with nothing active... How would your phone even know the power button was pressed? How would power button do one thing, but the bootloader key stroke combo (power and vol down at the same time) boot to a different mode? How does power button require being held down and time how long?

The hardware the power buttons attach to sit active and watch for button presses. When it sees the proper combination It will tell the "motherboard" its time to power up.

But still, It just can't be android... Android is stored on your internal SD card, which is partitioned... The data is split up into different chunks and the phone does not even know what chunk the system is in.

So motherboard starts to initialize very basic stuff. It will find its CPU, and will find storage, ect...

When it finds the storage, it will look for a special flagged partition that contains a simple program, the bootloader.

Bootloader is not android and almost has nothing to do with android, the system partition... whatever. Its running on VERY minimal hardware (hence when your in bootloader mode, you use the volume keys to scroll up and down... touch isn't loaded yet).

As long as bootloader is not broken/corrupt/erased and is not locked... Your pretty much safe. It has basic tools to receive data from a computer via fastboot, it can mount/write/wipe other partitions.

It also knows where your kernel is, and where your recovery is. Typically it will automatically just load the android kernel, which will continue to initialize the rest of your hardware, and and get all the software that gives you a user interface and control going.

It can also boot into recovery mode instead of booting into android. Recovery mode is yet another self contained program/operating system/partition that runs independent of android. It offers more interface and functionality then bootloader mode, but is still basic. I am sure you remember when recovery didn't used the touch screen either... This was because the factory touch screen drivers had not been loaded yet, the teams that write these recovery programs eventually included software to instruct the system how to read touch input though.

The point is the phone boots and initially only knows/needs/cares about the partition called "bootloader", which has a self contained program that has basic recovery options when paired with a computer and fastboot.

That bootloader looks for the partition "boot" which contains your kernel which will load the android OS off "system", and your personal data/preference off "userdata"

OR

The bootloader can load your custom recovery off the "recovery" partition, which can mount/read/write most other partitions.

The warnings about not wiping system were likely based off the idea that you needed to boot into android in order to download a rom to flash... but really you should always have a backup that you have made at a point when your system was working good stored on your "userdata" partition, or on an external SD card if you phone supports it.

However lacking those two options, at some point in the past you may have had trouble... But TWRP has supported MTP transfer for a while now, and failing that the sideload command, that flashes a rom from your computer via ADB has been supported for quite a few version, and even before that (starting in 2014 with TWRP 2.8.0.0) ADB was supported so the "adb push" command could be used to send data to a phone with no rom on it.

ANY of the above paragraph only really matters on a phone with a locked bootloader and custom recovery installed though, which is why people point the the nexus as being different (even though other phones have unlocked bootloaders). As long as you have a factory image of the phone, fastboot can be used to re-write the partitions to the phone without it even having a custom recovery (that how your custom recovery likely got on your phone in the first place... the same can be done for system or boot as well as the other partitions too).

Phones with a locked bootloader and/or no publicly released factory images are probably why you heard this warning in the first place.